[2023-06-18 10:25:11,713] [INFO] DFAST_QC pipeline started.
[2023-06-18 10:25:11,715] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 10:25:11,715] [INFO] DQC Reference Directory: /var/lib/cwl/stgc5109a53-d14b-4790-96f6-a16ecacace18/dqc_reference
[2023-06-18 10:25:14,946] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 10:25:14,947] [INFO] Task started: Prodigal
[2023-06-18 10:25:14,948] [INFO] Running command: gunzip -c /var/lib/cwl/stgb47f6254-5b3d-4bc3-ac63-05c0abbf9cd8/GCA_937136445.1_SRR4030105_bin.112_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_937136445.1_SRR4030105_bin.112_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_937136445.1_SRR4030105_bin.112_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 10:25:33,365] [INFO] Task succeeded: Prodigal
[2023-06-18 10:25:33,366] [INFO] Task started: HMMsearch
[2023-06-18 10:25:33,366] [INFO] Running command: hmmsearch --tblout GCA_937136445.1_SRR4030105_bin.112_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc5109a53-d14b-4790-96f6-a16ecacace18/dqc_reference/reference_markers.hmm GCA_937136445.1_SRR4030105_bin.112_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-18 10:25:33,600] [INFO] Task succeeded: HMMsearch
[2023-06-18 10:25:33,601] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgb47f6254-5b3d-4bc3-ac63-05c0abbf9cd8/GCA_937136445.1_SRR4030105_bin.112_CONCOCT_v1.1_MAG_genomic.fna.gz]
[2023-06-18 10:25:33,640] [INFO] Query marker FASTA was written to GCA_937136445.1_SRR4030105_bin.112_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-18 10:25:33,640] [INFO] Task started: Blastn
[2023-06-18 10:25:33,641] [INFO] Running command: blastn -query GCA_937136445.1_SRR4030105_bin.112_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgc5109a53-d14b-4790-96f6-a16ecacace18/dqc_reference/reference_markers.fasta -out GCA_937136445.1_SRR4030105_bin.112_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 10:25:34,229] [INFO] Task succeeded: Blastn
[2023-06-18 10:25:34,233] [INFO] Selected 18 target genomes.
[2023-06-18 10:25:34,234] [INFO] Target genome list was writen to GCA_937136445.1_SRR4030105_bin.112_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-18 10:25:34,264] [INFO] Task started: fastANI
[2023-06-18 10:25:34,264] [INFO] Running command: fastANI --query /var/lib/cwl/stgb47f6254-5b3d-4bc3-ac63-05c0abbf9cd8/GCA_937136445.1_SRR4030105_bin.112_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937136445.1_SRR4030105_bin.112_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_937136445.1_SRR4030105_bin.112_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 10:25:48,915] [INFO] Task succeeded: fastANI
[2023-06-18 10:25:48,916] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc5109a53-d14b-4790-96f6-a16ecacace18/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 10:25:48,916] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc5109a53-d14b-4790-96f6-a16ecacace18/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 10:25:48,924] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 10:25:48,924] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 10:25:48,924] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Longimicrobium terrae	strain=CB-286315	GCA_013000925.1	1639882	1639882	type	True	75.7808	68	822	95	below_threshold
Longimicrobium terrae	strain=CECT 8660	GCA_014198875.1	1639882	1639882	type	True	75.747	70	822	95	below_threshold
Longimicrobium terrae	strain=DSM 29007	GCA_014202995.1	1639882	1639882	type	True	75.7124	72	822	95	below_threshold
Streptomyces aidingensis	strain=CGMCC 4.5739	GCA_900112355.1	910347	910347	type	True	74.8877	70	822	95	below_threshold
Streptomyces alboflavus	strain=NRRL B-2373	GCA_000716675.1	67267	67267	type	True	74.725	78	822	95	below_threshold
Streptomyces flavofungini	strain=JCM 4753	GCA_016411765.1	68200	68200	type	True	74.7247	68	822	95	below_threshold
Streptomyces flavofungini	strain=JCM 4753	GCA_014650815.1	68200	68200	type	True	74.7222	67	822	95	below_threshold
Streptosporangium pseudovulgare	strain=JCM 3115	GCA_014648055.1	35765	35765	type	True	74.575	99	822	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 10:25:48,927] [INFO] DFAST Taxonomy check result was written to GCA_937136445.1_SRR4030105_bin.112_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-18 10:25:48,928] [INFO] ===== Taxonomy check completed =====
[2023-06-18 10:25:48,928] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 10:25:48,928] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc5109a53-d14b-4790-96f6-a16ecacace18/dqc_reference/checkm_data
[2023-06-18 10:25:48,930] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 10:25:48,976] [INFO] Task started: CheckM
[2023-06-18 10:25:48,977] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937136445.1_SRR4030105_bin.112_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937136445.1_SRR4030105_bin.112_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_937136445.1_SRR4030105_bin.112_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-18 10:26:38,643] [INFO] Task succeeded: CheckM
[2023-06-18 10:26:38,645] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-18 10:26:38,680] [INFO] ===== Completeness check finished =====
[2023-06-18 10:26:38,680] [INFO] ===== Start GTDB Search =====
[2023-06-18 10:26:38,681] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937136445.1_SRR4030105_bin.112_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-18 10:26:38,681] [INFO] Task started: Blastn
[2023-06-18 10:26:38,681] [INFO] Running command: blastn -query GCA_937136445.1_SRR4030105_bin.112_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgc5109a53-d14b-4790-96f6-a16ecacace18/dqc_reference/reference_markers_gtdb.fasta -out GCA_937136445.1_SRR4030105_bin.112_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 10:26:39,353] [INFO] Task succeeded: Blastn
[2023-06-18 10:26:39,359] [INFO] Selected 13 target genomes.
[2023-06-18 10:26:39,359] [INFO] Target genome list was writen to GCA_937136445.1_SRR4030105_bin.112_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 10:26:39,367] [INFO] Task started: fastANI
[2023-06-18 10:26:39,368] [INFO] Running command: fastANI --query /var/lib/cwl/stgb47f6254-5b3d-4bc3-ac63-05c0abbf9cd8/GCA_937136445.1_SRR4030105_bin.112_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937136445.1_SRR4030105_bin.112_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_937136445.1_SRR4030105_bin.112_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 10:26:47,972] [INFO] Task succeeded: fastANI
[2023-06-18 10:26:47,987] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-18 10:26:47,987] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_015492755.1	s__S146-37 sp015492755	77.7624	170	822	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__S146-37	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003559555.1	s__PWLA01 sp003559555	77.1655	123	822	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__PWLA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013002885.1	s__UBA2589 sp013002885	77.0784	136	822	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__UBA2589	95.0	99.00	99.00	0.85	0.85	2	-
GCA_007695195.1	s__PWLA01 sp007695195	76.9677	129	822	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__PWLA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007130605.1	s__SLBA01 sp007130605	76.8278	112	822	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__SLBA01	95.0	99.40	99.31	0.83	0.83	4	-
GCA_007120305.1	s__SKNW01 sp007120305	76.8154	93	822	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__SKNW01	95.0	99.60	99.60	0.85	0.85	2	-
GCA_007121775.1	s__PWLA01 sp007121775	76.744	102	822	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__PWLA01	95.0	99.55	99.40	0.89	0.80	6	-
GCA_007692665.1	s__SKNW01 sp007692665	76.581	143	822	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__SKNW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016873995.1	s__UBA2982 sp016873995	76.4908	90	822	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__UBA2982	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009692205.1	s__UBA2982 sp009692205	76.4584	78	822	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__UBA2982	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003248075.1	s__SZUA-318 sp003248075	76.4339	145	822	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__SZUA-318	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007129525.1	s__PWLA01 sp007129525	76.3914	87	822	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__PWLA01	95.0	98.95	98.95	0.75	0.75	2	-
GCA_015664885.1	s__UBA1138 sp003447875	76.1176	67	822	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__UBA1138	95.0	99.72	99.64	0.94	0.92	3	-
--------------------------------------------------------------------------------
[2023-06-18 10:26:47,989] [INFO] GTDB search result was written to GCA_937136445.1_SRR4030105_bin.112_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-18 10:26:47,990] [INFO] ===== GTDB Search completed =====
[2023-06-18 10:26:47,993] [INFO] DFAST_QC result json was written to GCA_937136445.1_SRR4030105_bin.112_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-18 10:26:47,993] [INFO] DFAST_QC completed!
[2023-06-18 10:26:47,993] [INFO] Total running time: 0h1m36s